Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches
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Universidade Federal de Minas Gerais
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Artigo de periódico
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Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen
bonding and stacking interactions are strongly dependent on the identity of the neighbouring base pairs.
As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs,
only a fraction of these have been studied in varying experiments or theoretical models. Here, we report
on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in
nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch
combinations, including single, double and triple mismatches were covered. These were compared with
64 sequences containing all combinations of canonical base pairs in the same location under the same
conditions. For a substantial number of single mismatch configurations, 15%, the measured melting
temperatures were higher than the least stable AT base pair. The mesoscopic calculation, using the
Peyrard–Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-
site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking.
Our results confirm many of the known properties of mismatches, including the peculiar sheared
stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches
present strong hydrogen bonding when flanked on both sites by other mismatches. To highlight the
applicability of our results, we discuss a number of practical situations such as enzyme binding affinities,
thymine DNA glycosylase repair activity, and trinucleotide repeat expansions.
Abstract
Assunto
DNA, Medição de temperatura
Palavras-chave
DNA, Melting temperature measurement, Mesoscopic evaluation
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Endereço externo
https://pubs.rsc.org/en/content/articlelanding/2020/SC/D0SC01700K